5X3F | pdb_00005x3f

Crystal structure of the YgjG-Protein A-Zpa963-PKA catalytic domain

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Protein kinase-like (PK-like)	8040503	3000066	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Bacterial immunoglobulin/albumin-binding domains	8091639	3001373	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8098688	3000954	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	B,Pkinase_Tyr	e5x3fB1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: B,Pkinase_Tyr	ECOD (1.6)
A	B	e5x3fA3	A: alpha bundles	X: immunoglobulin/albumin-binding domain-like	H: Bacterial immunoglobulin/albumin-binding domains (From Topology)	T: Bacterial immunoglobulin/albumin-binding domains	F: B	ECOD (1.6)
A	Aminotran_3_C	e5x3fA2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: Aminotran_3_C	ECOD (1.6)
A	Aminotran_3_N	e5x3fA1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_3_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
B	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (utative)
A	1.20.5.420	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Immunoglobulin FC, subunit C	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain		Domain
A	PF02216	B domain (B)	B domain	This family contains the B domain of Staphylococcal protein A, which specifically binds to the Fc portion of immunoglobulin G.	Domain
A	PF00202	Aminotransferase class-III (Aminotran_3)	Aminotransferase class-III		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Zpa963,cAMP-dependent protein kinase catalytic subunit alpha	cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding protein domain specific binding protein serine/threonine/tyrosine kinase activity protein serine/threonine kinase activity cyclic nucleotide-dependent protein kinase activity cAMP-dependent protein kinase activity protein serine kinase activity magnesium ion binding kinase binding protein kinase binding protein kinase A binding protein kinase A regulatory subunit binding	developmental process spermatid development spermatid differentiation sexual reproduction cellular developmental process spermatogenesis reproductive process multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental maturation developmental process involved in reproduction gamete generation male gamete generation sperm capacitation developmental process spermatid development spermatid differentiation sexual reproduction cellular developmental process spermatogenesis reproductive process multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental maturation developmental process involved in reproduction gamete generation male gamete generation sperm capacitation anatomical structure maturation cell differentiation anatomical structure development germ cell development cellular process cell maturation cellular localization establishment of protein localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport intracellular transport protein export from nucleus establishment of localization localization protein transport establishment of localization in cell macromolecule localization intracellular protein localization nuclear export intracellular protein transport cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus regulation of localization import into cell positive regulation of cellular component organization regulation of cellular process regulation of cellular component organization positive regulation of biological process vesicle-mediated transport cellular component organization positive regulation of endocytosis phagocytosis cellular component organization or biogenesis positive regulation of cellular process regulation of endocytosis regulation of biological process regulation of transport biological regulation regulation of phagocytosis regulation of vesicle-mediated transport positive regulation of phagocytosis positive regulation of transport endocytosis RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process metabolic process macromolecule metabolic process RNA processing multicellular organismal process embryonic epithelial tube formation chordate embryonic development tube formation embryo development multicellular organism development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching epithelial tube morphogenesis system development morphogenesis of embryonic epithelium epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium nervous system development tissue development anatomical structure morphogenesis tissue morphogenesis neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure trans-synaptic signaling regulation of signaling modulation of chemical synaptic transmission signaling cell-cell signaling chemical synaptic transmission cell communication synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication postsynaptic modulation of chemical synaptic transmission protein phosphorylation phosphorylation peptidyl-serine modification peptidyl-serine phosphorylation macromolecule modification peptidyl-amino acid modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process catabolic process proteolysis involved in protein catabolic process macromolecule catabolic process regulation of primary metabolic process regulation of proteolysis involved in protein catabolic process regulation of proteolysis proteolysis regulation of protein metabolic process proteasomal protein catabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process regulation of proteasomal protein catabolic process regulation of metabolic process regulation of protein catabolic process negative regulation of biological process negative regulation of RNA biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process formation of primary germ layer mesoderm morphogenesis gastrulation mesoderm formation mesoderm development potassium ion homeostasis inorganic ion homeostasis homeostatic process cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis intracellular potassium ion homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis regulation of osteoblast differentiation regulation of developmental process regulation of cell differentiation osteoblast differentiation ossification monosaccharide metabolic process gluconeogenesis positive regulation of metabolic process regulation of small molecule metabolic process positive regulation of biosynthetic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process positive regulation of gluconeogenesis carbohydrate metabolic process small molecule biosynthetic process carbohydrate biosynthetic process hexose metabolic process monosaccharide biosynthetic process hexose biosynthetic process positive regulation of glucose metabolic process regulation of gluconeogenesis positive regulation of carbohydrate metabolic process regulation of carbohydrate biosynthetic process positive regulation of small molecule metabolic process glucose metabolic process response to oxygen-containing compound cellular response to glucose stimulus intracellular glucose homeostasis cellular response to oxygen-containing compound response to hexose cellular response to carbohydrate stimulus cellular response to chemical stimulus response to monosaccharide response to carbohydrate response to glucose response to chemical glucose homeostasis carbohydrate homeostasis cellular response to hexose stimulus cellular response to monosaccharide stimulus cellular response to nitrogen compound response to endogenous stimulus response to peptide hormone cellular response to peptide hormone stimulus response to nitrogen compound response to glucagon cellular response to glucagon stimulus cellular response to endogenous stimulus response to hormone cellular response to hormone stimulus regulation of steroid biosynthetic process regulation of cholesterol biosynthetic process regulation of cholesterol metabolic process steroid metabolic process regulation of lipid metabolic process sterol metabolic process cholesterol metabolic process lipid biosynthetic process alcohol metabolic process positive regulation of lipid metabolic process steroid biosynthetic process secondary alcohol biosynthetic process regulation of alcohol biosynthetic process regulation of steroid metabolic process cholesterol biosynthetic process positive regulation of cholesterol biosynthetic process secondary alcohol metabolic process positive regulation of steroid biosynthetic process sterol biosynthetic process positive regulation of lipid biosynthetic process regulation of sterol biosynthetic process alcohol biosynthetic process positive regulation of cholesterol metabolic process positive regulation of steroid metabolic process regulation of lipid biosynthetic process positive regulation of alcohol biosynthetic process positive regulation of sterol biosynthetic process lipid metabolic process bicellular tight junction assembly regulation of bicellular tight junction assembly tight junction organization apical junction assembly regulation of cellular component biogenesis cellular component biogenesis regulation of cell junction assembly cell junction organization cellular component assembly cell junction assembly tight junction assembly cell-cell junction assembly cell-cell junction organization negative regulation of signaling regulation of signal transduction negative regulation of cell communication negative regulation of smoothened signaling pathway signal transduction regulation of smoothened signaling pathway cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction smoothened signaling pathway regulation of response to stimulus regulation of protein maturation protein maturation regulation of protein processing protein processing adenylate cyclase-activating G protein-coupled receptor signaling pathway adenylate cyclase-modulating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway regulation of protein localization positive regulation of nucleocytoplasmic transport positive regulation of establishment of protein localization positive regulation of protein transport positive regulation of intracellular transport regulation of protein export from nucleus regulation of intracellular transport regulation of establishment of protein localization regulation of nucleocytoplasmic transport regulation of protein transport positive regulation of protein export from nucleus regulation of cellular localization positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport protein localization to organelle protein localization to lipid droplet intracellular signal transduction cAMP/PKA signal transduction intracellular signaling cassette adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway cellular response to parathyroid hormone stimulus response to parathyroid hormone ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration negative regulation of small molecule metabolic process negative regulation of glycolytic process oxoacid metabolic process carbohydrate catabolic process organophosphate catabolic process carbohydrate derivative metabolic process regulation of generation of precursor metabolites and energy nucleoside phosphate catabolic process organic acid metabolic process negative regulation of ATP metabolic process regulation of ATP metabolic process regulation of purine nucleotide catabolic process negative regulation of nucleotide metabolic process glycolytic process regulation of nucleotide metabolic process pyridine-containing compound metabolic process purine ribonucleotide catabolic process negative regulation of carbohydrate metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process pyruvate metabolic process regulation of carbohydrate catabolic process negative regulation of purine nucleotide catabolic process purine nucleoside diphosphate metabolic process purine-containing compound catabolic process nucleotide metabolic process regulation of purine nucleotide metabolic process nucleobase-containing compound catabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process regulation of nucleotide catabolic process regulation of phosphorus metabolic process nucleoside triphosphate metabolic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process cellular respiration ATP metabolic process negative regulation of purine nucleotide metabolic process energy derivation by oxidation of organic compounds negative regulation of phosphate metabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process nucleotide catabolic process negative regulation of nucleotide catabolic process negative regulation of catabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process carbohydrate derivative catabolic process regulation of glycolytic process through fructose-6-phosphate ADP catabolic process carboxylic acid metabolic process generation of precursor metabolites and energy regulation of glycolytic process purine-containing compound metabolic process ADP metabolic process organophosphate metabolic process negative regulation of phosphorus metabolic process purine ribonucleoside diphosphate metabolic process purine ribonucleoside diphosphate catabolic process negative regulation of glycolytic process through fructose-6-phosphate glycolytic process through fructose-6-phosphate negative regulation of intracellular signal transduction negative regulation of TORC1 signaling regulation of intracellular signal transduction negative regulation of TOR signaling regulation of TORC1 signaling TOR signaling regulation of TOR signaling TORC1 signaling cellular response to cold response to cold cell cycle regulation of cell cycle positive regulation of cell communication positive regulation of insulin secretion regulation of biological quality regulation of peptide hormone secretion regulation of hormone levels positive regulation of peptide hormone secretion establishment of protein localization to extracellular region protein secretion regulation of protein secretion regulation of secretion regulation of hormone secretion regulation of peptide secretion positive regulation of secretion by cell hormone secretion protein localization to extracellular region peptide secretion regulation of secretion by cell secretion by cell positive regulation of hormone secretion positive regulation of secretion amide transport signal release positive regulation of peptide secretion secretion regulation of peptide transport export from cell positive regulation of protein secretion peptide transport regulation of insulin secretion peptide hormone secretion hormone transport insulin secretion positive regulation of signaling	membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium intracellular membraneless organelle cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection intracellular organelle cell projection cellular anatomical structure cytoskeleton organelle membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium intracellular membraneless organelle cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection intracellular organelle cell projection cellular anatomical structure cytoskeleton organelle membraneless organelle cytoplasm nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule nuclear body nucleoplasm organelle lumen supramolecular complex nuclear ribonucleoprotein granule nuclear lumen cytosol 9+2 motile cilium sperm flagellum motile cilium sperm midpiece synapse cell junction glutamatergic synapse neuromuscular junction perinuclear region of cytoplasm postsynapse acrosomal vesicle intracellular vesicle endomembrane system cytoplasmic vesicle secretory granule secretory vesicle vesicle mitochondrion centrosome microtubule organizing center microtubule cytoskeleton cell periphery plasma membrane membrane ciliary base protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex cAMP-dependent protein kinase complex serine/threonine protein kinase complex transferase complex intracellular protein-containing complex membrane microdomain membrane raft plasma membrane raft plasma membrane region
A	Putrescine aminotransferase,Immunoglobulin G-binding protein A	protein-containing complex binding binding immunoglobulin binding IgG binding transferase activity, transferring nitrogenous groups transaminase activity transferase activity catalytic activity diamine transaminase activity putrescine--2-oxoglutarate transaminase activity identical protein binding protein binding protein homodimerization activity protein dimerization activity protein-containing complex binding binding immunoglobulin binding IgG binding transferase activity, transferring nitrogenous groups transaminase activity transferase activity catalytic activity diamine transaminase activity putrescine--2-oxoglutarate transaminase activity identical protein binding protein binding protein homodimerization activity protein dimerization activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding anion binding heterocyclic compound binding small molecule binding	lysine metabolic process catabolic process oxoacid metabolic process lysine catabolic process L-lysine catabolic process L-amino acid catabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process lysine metabolic process catabolic process oxoacid metabolic process lysine catabolic process L-lysine catabolic process L-amino acid catabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process carboxylic acid catabolic process metabolic process cellular process small molecule metabolic process small molecule catabolic process amino acid catabolic process polyamine metabolic process biogenic amine catabolic process amine metabolic process putrescine catabolic process putrescine metabolic process polyamine catabolic process biogenic amine metabolic process amine catabolic process	cellular anatomical structure extracellular region intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR000719	Protein kinase domain	Domain
B	IPR044109	cAMP-dependent protein kinase catalytic subunit	Family
B	IPR017441	Protein kinase, ATP binding site	Binding Site
B	IPR000961	AGC-kinase, C-terminal	Domain
B	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
B	IPR008271	Serine/threonine-protein kinase, active site	Active Site
A	IPR009063	Immunoglobulin/albumin-binding domain superfamily	Homologous Superfamily
A	IPR005877	YSIRK Gram-positive signal peptide	Domain
A	IPR036779	LysM domain superfamily	Homologous Superfamily
A	IPR005038	Octapeptide repeat	Repeat
A	IPR003132	Protein A, Ig-binding domain	Domain
A	IPR018392	LysM domain	Domain
A	IPR019931	LPXTG cell wall anchor domain	Domain
A	IPR049704	Aminotransferases class-III pyridoxal-phosphate attachment site	Conserved Site
A	IPR050103	Class-III Pyridoxal-phosphate-dependent Aminotransferase	Family
A	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A	IPR017747	Putrescine aminotransferase	Family
A	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A	IPR005814	Aminotransferase class-III	Family